SSBD:database

Key Organism Strain Cell Line Gene Symbol Protein name Protein tag Reporter Project ID Dataset ID Title Description Data Type Gene Ontology Biological Imaging Methods Method Summary Paper Information Medical Subject Headlines Person

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29-Ke-SeeDB2

https://ssbd.riken.jp/database/29-Ke-SeeDB2/

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ssbd-repos-000029

https://ssbd.riken.jp/repository/29/

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2017-10-03

2018-11-15

CC BY

Image data based on Experiment

58 ( Image datasets: 58, Quantitative data datasets: 0 )

30.2 GB ( Image datasets: 30.2 GB, Quantitative data datasets: 0 bytes )

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Drosophila melanogaster, Homo sapiens, Mus musculus

HEK293T

Thy1

H2B, membrane, mitochondria, nucleus

EGFP, YFP

DAPI, MitoTracker, anti-alpha-tubulin, anti-kinetochore

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neuron structure

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XY: 0.025 micrometer/pixel, Z: 0.109 micrometer/slice, XY: 1.137 micrometer/pixel, Z: 0.786 micrometer/slice, XY: 0.994 micrometer/pixel, Z: 5.0 micrometer/slice, XY: 0.079 micrometer/pixel, Z: 0.4 micrometer/slice, XY: 1.590 micrometer/pixel, Z: 40 micrometer/slice, XY: 0.043 micrometer/pixel, Z: 0.25 micrometer/slice, XY: 0.043 micrometer/pixel, Z: 0.18 micrometer/slice, XY: 0.200 micrometer/pixel, Z: 0.999 micrometer/slice, XY: 0.041 micrometer/pixel, Z: 0.167 micrometer/slice, XY: 0.043 micrometer/pixel, Z: 0.100 micrometer/slice, XY: 1.435 micrometer/pixel, Z: 1.999 micrometer/slice, XY: 0.200 micrometer/pixel, Z: 0.500 micrometer/slice, XY: 0.041 micrometer/pixel, Z: 0.25 micrometer/slice

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Other

ConfocalMicroscope

LaserScanningConfocalMicroscopy

Fluorescence

Olympus FV-OSR super-resolution system, Olympus FV1000MPE (two-photon), Carl Zeiss ELYRA PS.1 (SR-SIM), Olympus FV1000MPE (confocal), Carl Zeiss Airyscan super-resolution, Leica TCS SP8 DLS (light-sheet)

EM-CCD, GaAsP, Airyscan, digital CMOS

Olympus UPLSAPO 10x/0.3 W, customized DLS lens, Carl Zeiss Plan-Apochromat 63x/1.4 O DIC M27, Olympus UPLSAPO 63x/1.4 O, Leica HC PL Apo 63x/1.3 glycerol, Olympus XLSLPLN25XGMP 25x/0.9 multi, Carl Zeiss alpha Plan-Apochromat 100x/1.46 O, Olympus UPLSAPO 100x/1.4 O, Olympus UPLSAPO 63x/1.3 glycerol, Carl Zeiss C-Apochromat 40x/1.2 W Korr M27

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Meng-Tsen Ke, Yasuhiro Nakai, Satoshi Fujimoto, Rie Takayama, Shuhei Yoshida, Tomoya S Kitajima, Makoto Sato, Takeshi Imai (2016) Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent., Cell reports, Volume 14, Number 11, pp. 2718-32

Published in 2016 Mar 22 (Electronic publication in March 10, 2016, midnight )

• doi: 10.1016/j.celrep.2016.02.057
• pmid: 26972009
  

(Abstract) Super-resolution imaging deep inside tissues has been challenging, as it is extremely sensitive to light scattering and spherical aberrations. Here, we report an optimized optical clearing agent for high-resolution fluorescence imaging (SeeDB2). SeeDB2 matches the refractive indices of fixed tissues to that of immersion oil (1.518), thus minimizing both light scattering and spherical aberrations. During the clearing process, fine morphology and fluorescent proteins were highly preserved. SeeDB2 enabled super-resolution microscopy of various tissue samples up to a depth of >100 mum, an order of magnitude deeper than previously possible under standard mounting conditions. Using this approach, we demonstrate accumulation of inhibitory synapses on spine heads in NMDA-receptor-deficient neurons. In the fly medulla, we found unexpected heterogeneity in axon bouton orientations among Mi1 neurons, a part of the motion detection circuitry. Thus, volumetric super-resolution microscopy of cleared tissues is a powerful strategy in connectomic studies at synaptic levels.

(MeSH Terms)

• Animals
• Brain/anatomy & histology
• Brain/metabolism
• Brain Mapping
• Iohexol/chemistry
• Mice
• Microscopy, Fluorescence[major]
• Neurons/physiology[major]
• Receptors, N-Methyl-D-Aspartate/deficiency
• Receptors, N-Methyl-D-Aspartate/genetics
• Refractometry
• Saponins/chemistry
• Synapses/chemistry
• Synapses/metabolism

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Takeshi Imai , RIKEN , Center for Developmental Biology , Laboratory for Sensory Circuit Formation

Meng-Tsen Ke, Yasuhiro Nakai, Satoshi Fujimoto, Rie Takayama, Shuhei Yoshida, Tomoya S. Kitajima, Makoto Sato, Takeshi Imai

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